16-11095291-G-C

Position:

• chr16-11095291-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.2117-25324G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,988 control chromosomes in the GnomAD database, including 19,998 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (19998 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

CLEC16A (HGNC:29013): (C-type lectin domain containing 16A) This gene encodes a member of the C-type lectin domain containing family. Single nucleotide polymorphisms in introns of this gene have been associated with diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2117-25324G>C		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2117-25324G>C		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76164 AN: 151870 Hom.: 19952 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.509

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.502 AC: 76267 AN: 151988 Hom.: 19998 Cov.: 31 AF XY: 0.499 AC XY: 37033 AN XY: 74284

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.514

Alfa AF: 0.472 Hom.: 2196

Bravo AF: 0.511

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12917716; hg19: chr16-11189148;